Structure of PDB 7zyt Chain A Binding Site BS01

Receptor Information

>7zyt Chain A (length=472) Species: 9606 (Homo sapiens)

QPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIP
SKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGG
IAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEV
TPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGA
DVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDG
KIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRI
PVNTRFQTKIPNIYATGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYN
CVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDG
MVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAH
PTLSEAFREANLAASFGKSINF

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 7zyt Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7zyt Structural and Biochemical Investigation of Selected Pathogenic Mutants of the Human Dihydrolipoamide Dehydrogenase.
• Resolution: 2.892 Å
• Binding residue (original residue number in PDB): I12 G15 P16 E36 K37 N38 G43 T44 C45 G49 C50 K54 Y118 G119 T148 G149 I189 F283 D320 M326 L327 A328 H329 Y359
• Binding residue (residue number reindexed from 1): I10 G13 P14 E34 K35 N36 G41 T42 C43 G47 C48 K52 Y116 G117 T146 G147 I187 F281 D318 M324 L325 A326 H327 Y357
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 1.8.1.4: dihydrolipoyl dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004148 dihydrolipoyl dehydrogenase activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
• GO:0034604 pyruvate dehydrogenase (NAD+) activity
• GO:0047101 branched-chain alpha-keto acid dehydrogenase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006086 acetyl-CoA biosynthetic process from pyruvate
• GO:0006120 mitochondrial electron transport, NADH to ubiquinone
• GO:0006508 proteolysis
• GO:0007369 gastrulation
• GO:0009083 branched-chain amino acid catabolic process
• GO:0042391 regulation of membrane potential
• GO:0048240 sperm capacitation

Cellular Component

• GO:0001669 acrosomal vesicle
• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005929 cilium
• GO:0031410 cytoplasmic vesicle
• GO:0031514 motile cilium
• GO:0043159 acrosomal matrix
• GO:0045252 oxoglutarate dehydrogenase complex
• GO:0045254 pyruvate dehydrogenase complex
• GO:0160157 branched-chain alpha-ketoacid dehydrogenase complex
• GO:0160167 oxoadipate dehydrogenase complex
• GO:1902493 acetyltransferase complex

External links

• PDB: RCSB:7zyt, PDBe:7zyt, PDBj:7zyt
• PDBsum: 7zyt
• PubMed: 37446004
• UniProt: P09622|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)